The Minato Project
by Lobasola
Summary: 7 year old Naruto gets the scare of a lifetime when he finds a naked man who calls him son. *Au-ish*
1. Secrets

Chapter 1: Secrets

Minato could be considered a genius. He was also considered to be one of the most powerful Shinobi in the five elemental Nations. The man had inspired fear and admiration during the Third Shinobi war and awe during his first day as Fourth Hokage. Minato's wife Kushina couldn't be more proud. That sissy she thought would be a weak shinobi turned the tables on them all. The village entered a relatively peaceful time during Yondaime's reign. That is until October 10th. The day Kushina and Minato's son would be born. It had been a terrible day. A joyful and sorrowful one. Minato and Kushina sacrificed everything to keep Naruto alive. Minato knew, that someday he would die. He knew it even before the Kyuubi attack. He knew that he had to take precautions in case that were to happen the moment Kushina told him she was pregnant.

So Minato, being the overprotective and slightly paranoid man he was…began a project. A secret project. The Yellow Flash researched and experimented. Spent countless hours creating his plan B. Using his own DNA, Minato created a clone that couldn't be dispelled. Made from his chakra as well as his own cells. His goal was to create a replacement for his future son in case of death. A replacement which would go to any and all lengths to keep the little boy inside his wife safe.

He knew if anyone found out, it would cause chaos, so he made sure to keep it under wraps from everyone. There had been one little problem however. The clone wasn't growing as fast as he originally predicted or wanted. After months of showing no signs of rapid growth, Minato decided to leave it be. The Yellow Flash took this dirty secret to his grave. It would stay that way for a long time…

* * *

Naruto was running. The little boy couldn't take the glares and insults he was being subjected to. 'Why do they hate me?' he asked himself. However, he had no answer for that. Naruto ran until he reached one of the abandoned training grounds. The forest was lush and mysterious and provided the perfect hiding place for the boy to cry his sorrows. The seven year old had recently been kicked out of the orphanage. The third Hokage had promised he would fix the situation soon.

'He better!' thought Naruto indignantly, 'I can't take one more day of this. Jiji better hurry ttebayo!'

Naruto walked aimlessly along the trees, looking around curiously. He hadn't been to this part of the village. Naruto made his way through the tree roots and grass until his foot touched something that wasn't dirt.

"Huh," Naruto hummed as he crouched on the ground. He knocked on the surface and was surprised to find that it was made of metal. He took some of the dirt, leaves, and roots out of the way. He made a face when he found that the ground looked exactly the same. Naruto looked around to see if there was anything else that looked suspicious. The blond couldn't find anything out of the ordinary. After hours of trying Naruto decided to go to sleep. He had no place to stay at the moment. He had spent two days on the street waiting for Sandaime-Jiji to fix something. Naruto leaned against a tree close to where the strange metal ground was. He was about to close his eyes when, suddenly, markings appeared behind him. Before the blond could see what they looked like, they disappeared.

Naruto shrugged and fell asleep.

The next day, Naruto decided to skip the academy all together. After all he had found something way more interesting. When the little ninja in training woke up the next morning, he found that the ground no longer looked the same as everything else. There was an entrance. Like one of the sewers around town. Naruto being the curious and hyperactive boy he was could not pass up this opportunity. The boy lifted the top off of the entrance and climbed down the ladder. The tunnel was standard, creepy and dark. There were arrows however. So Naruto followed the signs. At the end of the long hallway was a door. It looked rusted with a few coats of dust. Naruto slammed his body against the door a few times before it was knocked down.

"Ow man that really hurt…dattebayo…" Naruto panted.

The blond looked at the room he had uncovered. It was relatively normal. There was a table, some parchment, and scrolls. However, what made the room stand out was the giant test-tube. In that giant Test-tube was a very naked man. He was blond and slender. His skin was chalk white, from the lack of sunlight and his hair was long and unruly. If one were not careful and failed to notice his intimate parts, one would have assumed the man was a girl.

"Creepy much?" Naruto shuddered as he hesitantly stepped forward.

The boy reached the test-tube. Naruto touched the glass and a few markings appeared. The glass shattered, making Naruto stepped back a few feet to avoid getting hurt too badly. The contents of the tube came flooding out. Water of some sort. The unknown man dropped to the floor like a doll.

"Um…mister?" Naruto called.

The man moaned as his limbs twitched and his fingers moved involuntarily. Naruto carefully moved forward ignoring the slight sting from the scratches he had suffered from the shattering glass. He touched the man's shoulders and shook him.

"Hey mister! Wake up ttebayo!"

Cerulean eyes opened and met Naruto's. The man blinked a few times before sitting up. He touched Naruto's cheek and then his hair and stared into his eyes, with a deep, soulful, and analytical stare. Naruto felt like he was being picked apart. He was officially scared so he moved away. The man grabbed his arm and pulled him into a hug.

"You're my son," the man rasped, "Naruto. Naruto."

Naruto was officially stunned. What?!

* * *

"Hokage-sama!" Sandaime looked up from his paper work to find a frantic looking Iruka in front of him.

"Iruka-san," the old man acknowledge, "What troubles you? Is it Naruto-kun?"

"Yes!" replied the instructor, "he's not at school. He didn't show up today. I can't find him anywhere!"

The Third wasn't all that surprised. Naruto did ditch sometimes, however he was soon located. Regardless, Naruto was becoming stealthier by the day. Soon the Third feared the boy would give Chunins and ANBUs alike a run for their money.

"Alright, Iruka, let's calm down. I'm sure Naruto is fine. Go back to the academy. I will look for him myself."

Iruka seemed to be satisfied with that answer and shushined away. Sarutobi sighed and got up. He would have lecture Naruto again. He was slightly worried, but he was sure Naruto was in no danger. The old man got his crystal ball and watched.

* * *

Naruto ran. As soon as the strange test-tube man had said those words he took off running. He was currently hiding in an alleyway, hugging his hands and knees.

"That has to be the weirdest thing I've ever experienced in my short life ttebayo!" Naruto screamed.

Naruto watched as his scratches and cuts healed. He was unsure of what to do now. 'Maybe I can bother Sandaime-Jiji since it's too late for me to go to school…' Naruto stood up and ran to the Hokage's residence, ignoring the frigid glares he was receiving along the way.

* * *

"It looks like I won't have to look for him…" mused The Third.

* * *

The Test-tube man was left sitting there dumbly. He watched the boy run for the hills in fright. The man was hurt. But that didn't impede the man's reasoning. From the limited data he had, he gathered that his approach might have been too strange and slightly invasive. The man got up carefully and balanced himself before taking a few steps forward. All the man knew, was that he needed to take care of Naruto. Naruto was his son. He knew there was something else he was missing beneath the surface. More data he had yet to look through in his blank mind. However, That wasn't important to the blond man at the moment.

The Minato clone made his way through the dank tunnel and into the sunlight. He needed to find Naruto.

* * *

"Sandaime-Jiji!" Naruto stormed through the door, "When will I have a place to sleep?"

'Naruto-kun, I have arranged for an apartment to be assigned to you. It should be ready by tomorrow. There's no need to yell." Sarutobi blew a puff of smoke from his mouth. "Now, can you tell where you have been during the morning Naruto-kun?"

"I..well you see…" Naruto rambled looking away. He was a terrible liar.

Luckily he was saved by an ANBU at that moment.

"Hokage-sama," said the masked nin, "There is a naked man in the village sir."

Sarutobi Hiruzen wondered how long it would take for his heart to finally give way.

* * *

**AN: Well another story idea. However, I feel bad about Making Minato do the creepy experiment like Orochimaru. It was fun though XD.**


	2. Enter: Minato?

**A/N: Okay, thanks for the reviews! So to Start I would like to the pairing situation. I'm honestly not sure what to do. I honestly wasn't thinking on any particular pairing for Naruto. I don't particularly lean toward Yaoi either. ^^(I mean no harm promise XD). The Pairings I like are Naruhina or NaruSaku. Or even more disturbing would be NaruTsunade(lol time travel fics only). I take anything as long as it's not Yaoi(again I mean no harm or offense). Anyway, since Yommama3 requested the pairing first I'll make it Naruhina. As for Guest's doubts about this being a one shot…no it isn't. Okay then, lets start.**

* * *

Chapter 2: Enter: Minato?

Naruto froze at the mention of the naked man. Sarutobi noticed and dismissed the ANBU, after giving him orders to take the stranger into custody and bring him here, as well as clothing him. Hiruzen glanced at Naruto with a raised brow and shimmer of suspicion in his eyes.

"Is this in some way related to your brief disappearance?" The Third asked while smoking his pipe.

Naruto said nothing for a long while and then nodded. He kept quiet for a few minutes. How was he to tell his grand-father figure that he found a creepy naked man, who claimed to be Naruto's long deceased father? How could he tell the Sandaime that he was scared witless at the man's sudden approach?

"Jiji, " Naruto began taking a deep breath, "therewasasecretentrence-"

"Naruto-kun," interrupted the old man, "explain to me slowly."

Naruto nodded, "I was looking for a place to get away from the village, so I ran to the abandoned training grounds. I found this weird entrance and got into an underground tunnel that led me to a room that led me to this creepy naked man in a test-tube-"

"Naked man in a test-tube?" Sarutobi said incredulously. If Naruto had told him this earlier he would not have believed him. However, the first bit about the civilians he would have believed.

"Yes don't interrupt me dattebayo!" Naruto scolded, "anyway I was in this dark room and I got closer to the giant tube and I touched it and it opened and th-the man…I shook him awake and he…he hugged me and said I was his son! I got scared…there I said it ttebayo!"

Hiruzen was about to respond when the masked ninja from earlier appeared along with the man Naruto had claimed to have seen, this time the clone was clothed. Sarutobi's breath hitched. There, standing in front of him was a ghost. The ghost of a man he thought had been killed in the line of duty. The clone noticed Naruto in a corner and tried to get free from the ANBU's grip.

"Jiji?" Naruto called worriedly.

The Third willed for his breath to return and exhaled a hearty sigh. Hiruzen stared at the blond man carefully. "Who are you?"

The blond gave a polite smile as he finally noticed then old man, "I am Minato." He said simply.

Minato…there was no way this was Minato. Had Orochimaru been behind this? Hiruzen asked himself. The Third certainly didn't put it past the snake-sannin to pull off something like this. Sarutobi had been certain that all of his former student's experiments were discovered and destroyed. At least the non-human ones.

Somewhere else tenzou sneezed.

Sarutobi cleared his throat. His eyes never leaving the man. "That is not possible. Namikaze Minato is dead. He died 7 years ago." The Third said smoking from his pipe in an attempt to get his emotions under control. This whole situation as well as the fact that Naruto was here and would ask questions, was making him nervous.

"I'm Minato. Naruto's Father." The blond man said mechanically, "I would like for the ANBU to let go of me now Hokage-sama."

Further proof that this wasn't Minato. The man was treating Hiruzen like a stranger. An obstacle he had to overcome in order to get somewhere.

"I'm afraid that won't be possible." Hiruzen replied, making the clone's eyes narrow.

"Why is that? He's my flesh and blood. I am sure our DNA is compatible." said the adult blond.

"Jiji! Can you tell me what the heck is going on? Who's Minato Namikaze? Why's that man saying things like that!?" Naruto shouted.

The Hokage ignored Naruto's ramblings, which unnerved the young academy student. Sarutoi's attention remained fixed on Minato. "Well Minato-san…maybe it has to do with the fact that Naruto-kun found you in rather odd circumstances. Until I deem that you are not a threat to this village or Naruto-kun, you will by no means be close to him."

With the speed of cheetah, the clone turned and punched ANBU who held him. Naruto squeaked as the strange man picked him up and threw his body out the window. Other ANBU appeared but the clone quickly hopped onto another roof and darted away.

"HEY lemme go!" Naruto yelled squirming in clone Minato's grip.

"I am sorry but that will not be possible Naruto."

* * *

The Sandaime groaned. He was getting way too old for this job! He looked at the broken window and sighed. Then he looked at the ANBU who was just getting his composure back.

"I want you to get Inu here." Hiruzen barked. The ANBU obeyed and disappeared.

A few minutes later an ANBU in a dog mask appeared. He bowed and looked at Sandaime expectantly. "Hokage-sama."

"Inu, I need you to track and apprehend a man. He took Naruto with him. Just a fair warning however, do not let appearances fool you."

The ANBU nodded, though a bit perplexed by the Hokage's warning. Dog disappeared.

* * *

The Minato clone was just approaching the entrance of the village. He would take Naruto and run to the ends of the Earth if needed. When Minato saw the Hokage, he felt no familiar ties to the man. Though, he knew who it was. Sarutobi Hiruzen, rank, Hokage. The leader of the Leaf village. The clone also knew what the ANBU were and what Ninja's were. But, he had no memory. Just general information. It was different with Naruto. He felt something for the squirming boy in his arms.

The clone had no interest in the village whatsoever.

After passing the gate, the older blond felt a presence following them. It was another ANBU. Clone Minato picked up the speed, making Naruto yelp and clutch tightly to him. The clone didn't get too far though, as he dodged an incoming Kunai and lost balance falling to the ground.

"Ow!" Naruto groaned.

Inu hopped down from the trees, his eyes not believing what they were seeing.


	3. Tricks

**A/N: To my concerned readers XD relax~ I'm not going to focus on Naruhina. Naruhina isn't the focus of the story. Nor am I going to make little Naruto have lovey feelings. He's 7. The worst I'll do is hint at it very slightly(not very much, sorta like a friendship but that's it enough to support it but not...smother you with it lol). Thank you for your concern about this though I appreciate it. Don't worry, you guys can relax and get some popcorn *smiles***

* * *

Chapter 3: Tricks

Inu's face was crumpling under the mask. He was glad for the mask. It kept him from making a fool out of himself in front of the enemy. Inu debated what to do next. If he tried to attack he could hurt Naruto in the process...if he chased the Minato look alike would run away. Right now things were at a stand still. Thus Dog decided for dialogue.

"You are coming with me." said the ANBU

Minato frowned, "If I come Naruto will be taken from me right ANBU-san?"

"No," Dog bluffed quickly, "Not if you come with me peacefully. You are in no condition to fight now."

Minato surveyed what was said to him. The dog masked ninja was right. If he got into a fight, Naruto could get injured. Plus he had no weapons and not enough chakra to fight him with any jutsu. He would lose if he tried to fight. If he were to flee the ANBU would follow.

"Hai, I will come with you but Naruto stays with me." Minato warned.

Minato got on his feet with a frightened Naruto in his arms. The 7 year old couldn't decide which person to be scared of. The Inu ANBU or his supposed father. Both of them were leaking killing intent in waves and it was too much for the tiny blond to handle. Naruto gripped Minato's shirt instinctively and hid his face. Dog noticed and made himself calm down enough for the kid to breathe easier. Minato did the same.

* * *

The Third watched-from his crystal ball- Inu persuade the man into coming back. He could see that this man meant no harm to Naruto but he was still suspicious of his origins. When the trio made it to the village he sent for Iruka to come in. The academy was done for the day so he was free. Iruka appeared.

"Hokage-sama," the instructor addressed.

"Iruka-san, I need you to watch Naruto while I take care of some things. I will send for him to be brought to you later."

"Hai, I understand," with that Iruka disappeared.

* * *

"I'm sorry to have to do this…" Dog hit Minato in the back of the head and knocked him out as soon as the blond man let his guard drop. He carried the man with his right and Naruto with his left.

"ANBU-san…what's gonna happen to him?" Naruto asked finally gaining the courage to speak.

"He'll be under the Hokage's custody for a bit…" Dog said, "don't worry about it."

Dog used all of his strength to jump through the concrete roofs. It was a bit difficult carrying two people but he could manage. He entered through the window and dropped Minato like a sack of potatoes as he panted. "It's done Hokage-sama."

"Good, now I need you to get Naruto to Iruka-san and call Inoichi here. I need him." replied Hiruzen.

"Hai," Dog said as he flickered away.

Sarutobi then bent down picked a lock of the clone's hair. He called his secretary and demanded that some of his medic-nin take a look at this DNA sample to identify the double.

* * *

Minato's eyes fluttered as he regained consciousness. He was currently tide up. His hands and feet were strapped to a chair. He frowned, realizing the he had been played for a fool. His eyes skimmed the area. It was dimly lit room with no windows. His blue eyes watched as two figures stepped out of the darkness.

"I'm sorry it has come to this," said the man, whom he recognized as the Third. "but you have left me no choice. Minato-san."

"Where's Naruto," the blond spat.

"He's safe, I assure you." replied the Sandaine.

"Inoichi I want you to probe his mind, find out if he's a threat. Try to find memories. Survey his mind scape." Sarutobi ordered the man behind him. Inoichi was tall with pale blond hair and light pupiless eyes.

Inoichi nodded and got to work. The first thing Inochi noticed was concrete. The floor in the man's mind was made of concrete and resembled a narrow pathway. The mindscape was relatively empty. Just white space with a floor. The floor represented the foundation on which his mind was being built upon. There were no defenses or least he had not found any yet. It was odd. It…appeared as if Minato's mind was just developing.

"You don't belong here." Inoichi turned around, Minato was there.

'Looks like he's making defenses. At this rate, the mindscape won't be so empty anymore.' Thought the Yamanaka. "I don't want to fight, I'm just here to evaluate your situation."

"Leave then," Minato said coldly, "there's nothing here. I want nothing more than Naruto-kun's safety."

The ground below them expanded a bit more. It became wider until it was the size of a dance floor. "He will be safe…if you let look around more."

"He will only be safe with me," Minato stated, "I'm his Father."

Inoichi found that the double's statement seemed programmed. As if he was doing it out of reflex. But he could see that this man felt a genuine connection to Naruto. "If you are deemed safe by the Hokage perhaps he will allow you to get close to the kid." Inoichi bargained, "If you resist it will be to your disadvantage."

"I'm not falling for that bluff again, intruder-san," Minato said as he charged at the man. The clone's representation moved fast, unhindered by the limitations of the physical world. Here, Minato could fight. Inoichi was on his toes. The mind specialist was careful to dodge and counter the assaults. Minato's clone was skilled but he still wasn't as fast as his original. During an opening Inoichi managed to hit Minato in the stomach.

Inoichi sighed and wondered when he would be home to his wife and daughter. "Look…Minato-san…" Inoichi said carefully, "I don't want to fight with you. If you let me do my job I will leave."

Minato panted for a few moments. "I will let you proceed, but as soon as you're done, you will exit my mind immediately." Minato faded.

Inoichi watched as words appeared all around him. Pockets of information, all out of order. Floating listlessly amidst the empty white space. Inoichi deduced that, the clone's mind did have a defense after all, and that the appearance of Minato here wasn't a spur of the moment as he originally thought. The words floated all around him as if trying to find a place to occupy and settle. Inoichi walked forward, the floor expanding as he did so. Until he came to a white door. The Yamanaka opened it.

* * *

"Are you okay Naruto-kun?" asked Iruka concerned, the boy had been eerily quiet since the ANBU brought him a few hours ago. They were currently in Iruka's apartment. The sun was beginning to set, saying farewell to the village.

"Yeah!" Naruto said, grinning, but it didn't reach his eyes. The boy had been pondering the day's events. They bugged him. That man bugged him. "It's just been a really freaky day Iruka-sensei."

"Why is that?" asked Umino.

"I can't tell you. Inu-san said it was a secret. ttebayo!"

"Oh well," said Iruka, "Maybe I can take you to Ichiraku ramen? That will cheer you up?"

"Yeah! Definitely dattebayo!" Naruto jumped from the coach and ran out of the apartment.

"Hey wait for me!" Iruka followed.

* * *

Inu stayed close to the Sandaime and asked him question after question as soon as he was out of the interrogation room. His heart was pounding with disbelief, sadness, and curiosity. He felt disbelief because he knew for a fact his Sensei and his wife perished 7 years ago. He felt saddened because as soon as Inu put eyes on Minato's double, he was reminded of that tragic day. Curiosity, because he wanted to know just what the hell was going on.

"Please keep calm," admonished the Third as he walked briskly down the halls, "As soon as the tests I have assigned are done...and Naruto leads us to the place he found that man…we will know what exactly is going on."

Dog frowned under the mask as he followed, "I know," he said calmly but with a slight edge, "but he looks too much like…him…I can't possibly be at ease until this is over."

"I understand but we must be patient Kakashi-kun,"


End file.
